Add `gen3 run` Wrapper Command with `GEN3_TOKEN` Environment Variable Support

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.25.4

Notes to tag/commit: 1091867

Generated: 2024-12-11

New Features

• Adding Gen3 Wrapper command gen3 run that relays any command sent to it
  by adding GEN3_TOKEN env var. (#244)

4.25.4

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.25.3

Notes to tag/commit: 4.25.4

Generated: 2024-10-22

Dependency Updates

• update drsclient to 0.3.0 (#239)
• update pypfb to 0.5.30 (#239)

4.25.3

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.25.2

Notes to tag/commit: 4.25.3

Generated: 2024-10-04

Dependency Updates

• update dictionaryutils to 3.4.11 (for jsonschema updates) (#235)

4.25.2

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.25.1

Notes to tag/commit: 4.25.2

Generated: 2024-09-13

Improvements

• Gen3Submission.submit_record now prints API errors (#234)
• Updates docs for index create_record to reflect the correct type for authz.
  (#231)

New Features

• in case --endpoint is provided, we use endpoint to get files instead of
  look into the index (#225)

4.25.1

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.25.0

Notes to tag/commit: 4.25.1

Generated: 2024-06-26

Bug Fixes

• Fix Gen3Index create_record to return the created indexd record, rather
  than just the did, rev and base_id. (#228)

4.25.0

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.24.2

Notes to tag/commit: b6d6696

Generated: 2024-06-17

New Features

• download data from external repos (#220)

Improvements

• Remove Gen3Index.get_all_records unused start parameter (#224)

Auth fixes

Release Notes

For: uc-cdis/gen3sdk-python
Notes since tag: 4.24.1
Notes to tag/commit: 9852786
Generated: 2024-06-11

Bug Fixes

• don't attempt to use a refresh token if there isn't one available, warn
  instead of error (#223)

4.24.1

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.24.0

Notes to tag/commit: 4.24.1

Generated: 2024-06-06

Dependency Updates

• drsclient, indexclient, and pypfb dependencies updated to use PyPI
  published artifacts instead of github repositories (#213)

DOI fixes

Release Notes

For: uc-cdis/gen3sdk-python
Notes since tag: 4.23.1
Notes to tag/commit: c4d5e73
Generated: 2024-06-06

New Features

• Added function that scans user yaml files for security concerns (#219)

Breaking Changes

• DOI creation now defaults to the test DOI resolution URLs instead of
  production URLs. If you need production URLs, must provide explicit
  datacite_use_prod=True in mint_dois_for_discovery_datasets,
  use_prod=True in
  DigitalObjectIdentifier.from_datacite_create_doi_response,
  use_prod=True in DigitalObjectIdentifier( init (#215)

Bug Fixes

• correct metadata return to use original phsids for DOI retrieval from dbGaP
  API (#215)

Improvements

• allow overriding access token in auth function (#215)
• fix wrong argument name in documentation (#215)
• Github Action Workflow added to automatically push new releases to PyPI
  (#212)

4.23.1

Release Notes

For: uc-cdis/gen3sdk-python

Notes since tag: 4.23.0

Notes to tag/commit: 4.23.1

Generated: 2024-03-01

Improvements

• Github Action Workflow added to automatically push new releases to PyPI
  (#212)